From: JC Gumbart (gumbart_at_physics.gatech.edu)
Date: Tue Nov 01 2016 - 21:28:04 CDT
Yes, we use those files. We had to combine a few dihedrals, since NAMD doesn’t like multiple definitions with the same periodicity (it just uses the most recent one):
!C CT1 NH1 C -0.2000 1 0.00 ! C22STAR The forcefield as described in DESMOND contains
!C CT1 NH1 C -1.8250 1 90.00 ! C22STAR multiple dihedrals with the same periodicity.
!C CT1 NH1 C 0.0540 2 90.00 ! C22STAR Strictly speaking, this violates CHARMM
!C CT1 NH1 C -0.1090 1 150.00 ! C22STAR specifications.
!C CT1 NH1 C 0.0770 2 150.00 ! C22STAR This system reduces to that below:
!C CT1 NH1 C -0.0960 3 150.00 ! C22STAR
!C CT1 NH1 C -0.1060 4 150.00 ! C22STAR
C CT1 NH1 C 1.88246 1 266.784 ! C22STAR
C CT1 NH1 C 0.11403 2 125.788 ! C22STAR
C CT1 NH1 C -0.0960 3 150.000 ! C22STAR
C CT1 NH1 C -0.1060 4 150.000 ! C22STAR
And
!
!NH1 C CT1 NH1 0.6000 1 0.00 ! C22STAR
!NH1 C CT1 NH1 -2.2860 1 60.00 ! C22STAR The forcefield as described in DESMOND contains
!NH1 C CT1 NH1 -0.3620 2 60.00 ! C22STAR multiple dihedrals with the same periodicity.
!NH1 C CT1 NH1 0.0130 1 150.00 ! C22STAR Strictly speaking, this violates CHARMM
!NH1 C CT1 NH1 0.9420 2 150.00 ! C22STAR specifications.
!NH1 C CT1 NH1 0.2670 3 150.00 ! C22STAR This system reduces to that below:
!NH1 C CT1 NH1 -0.1270 4 150.00 ! C22STAR
!
NH1 C CT1 NH1 2.0496 1 -105.689 ! C22STAR
NH1 C CT1 NH1 1.0092 2 171.021 ! C22STAR
NH1 C CT1 NH1 0.2670 3 150.00 ! C22STAR
NH1 C CT1 NH1 -0.1270 4 150.00 ! C22STAR
And
!
!NH1 CT1 C N 0.6000 1 0.00 ! C22STAR
!NH1 CT1 C N -2.2860 1 60.00 ! C22STAR The forcefield as described in DESMOND contains
!NH1 CT1 C N -0.3620 2 60.00 ! C22STAR multiple dihedrals with the same periodicity.
!NH1 CT1 C N 0.0130 1 150.00 ! C22STAR Strictly speaking, this violates CHARMM
!NH1 CT1 C N 0.9420 2 150.00 ! C22STAR specifications.
!NH1 CT1 C N 0.2670 3 150.00 ! C22STAR This system reduces to that below:
!NH1 CT1 C N -0.1270 4 150.00 ! C22STAR
!
NH1 CT1 C N 2.0496 1 -105.689 ! C22STAR
NH1 CT1 C N 1.0092 2 171.021 ! C22STAR
NH1 CT1 C N 0.2670 3 150.00 ! C22STAR
NH1 CT1 C N -0.1270 4 150.00 ! C22STAR
!
Best,
JC
> On Nov 1, 2016, at 2:15 PM, Nicholas M. Glykos <glykos_at_mbg.duth.gr> wrote:
>
>
> Dear All,
>
> I was looking for an NAMD-compatible implementation of the CHARMM22-STAR
> force field and I came across a distribution of topology and parameter files
> from the ACEMD documentation at
>
> http://docs.acellera.com/acemd/usermanual/#charmm-force-field
>
> Does anybody have any experience -or other thoughts to share-
> about this implementation ?
>
> All the best,
> Nicholas
>
>
>
>
> --
>
> Nicholas M. Glykos, Department of Molecular Biology
> and Genetics, Democritus University of Thrace, University Campus,
> Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) +302551030620,
> Ext.77620, Tel (lab) +302551030615, http://utopia.duth.gr/glykos/
>
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